Alignments for a candidate for ilvI in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermus aquaticus YT-1

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_053767937.1 BVI061214_RS07970 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_001280255.1:WP_053767937.1
          Length = 561

 Score =  563 bits (1451), Expect = e-165
 Identities = 301/564 (53%), Positives = 387/564 (68%), Gaps = 16/564 (2%)

Query: 38  LTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAH 97
           + GA+A++++LE  GV+VIFG PGGA++P YD L+DS  +RH+LVRHEQG  HAA+ YA 
Sbjct: 1   MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSP-IRHILVRHEQGGIHAATAYAR 59

Query: 98  VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157
            +GRVGV MATSGPGA NLVT LADA MDS PVVAITG V R LIGTDAFQEAD++G+TM
Sbjct: 60  ASGRVGVVMATSGPGALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTM 119

Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217
           PITKHN+LV+  ++IPRV+ EAFHIA++GRPG VL+D+PKDV   + T  +   ++LPGY
Sbjct: 120 PITKHNYLVQDVNEIPRVVKEAFHIASTGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGY 179

Query: 218 KPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARG 277
           KP  + H +Q+  A   +  A +P+L VGGG     A  +L   AE TG+PV+TTLM  G
Sbjct: 180 KPTLRGHPKQIERALDALEKAERPILMVGGGAQHAHA--ELLAFAEKTGLPVITTLMGLG 237

Query: 278 AFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEA-KVIHAD 336
           AFP +H   LGMPGMHGTVAA  A+  +D+++A+G RFDDRVTGK+  FAP A  +IH D
Sbjct: 238 AFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHAHTIIHVD 297

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396
           IDPAEIGK     +PIVGD + V+ E++   +       + +A WW  L   R  YPL Y
Sbjct: 298 IDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAK------PLRLAAWWRELEEWRTRYPLRY 351

Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456
            P+    L    VI    E  G +A+   GVGQHQM+AAQ+    +PRS+L SGGLGTMG
Sbjct: 352 RPRP--HLQAPEVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMG 409

Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516
             +P A+GA+IA P   V   DGDG FQMT QELAT     +PVKV ++NNG LGMVRQW
Sbjct: 410 VGLPFAIGAQIARPEELVIDFDGDGSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQW 469

Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVV 576
           Q LF+A+RYS+  LA  +   PDF KLAEA G  G+R ER+ED+   + +A    D PVV
Sbjct: 470 QDLFHAKRYSEVYLADSN---PDFAKLAEAYGIKGVRVERKEDLKKGV-EAVLNADGPVV 525

Query: 577 IDFIVGADAQVWPMVAAGTSNDEI 600
            +F V  +  V+PM+ AG + +++
Sbjct: 526 AEFKVYHEEGVFPMIPAGGAAEDM 549


Lambda     K      H
   0.319    0.136    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1107
Number of extensions: 60
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 618
Length of database: 561
Length adjustment: 37
Effective length of query: 581
Effective length of database: 524
Effective search space:   304444
Effective search space used:   304444
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_053767937.1 BVI061214_RS07970 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.166477.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-244  797.9   0.0   2.6e-244  797.8   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053767937.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767937.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  797.8   0.0  2.6e-244  2.6e-244       1     555 [.       1     551 [.       1     553 [. 0.98

  Alignments for each domain:
  == domain 1  score: 797.8 bits;  conditional E-value: 2.6e-244
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +kgae+l+++l++egve++fG+PGGa++p ydalyds ++hilvrheq+ +haa  yarasG+vGvv+atsGP
  NCBI__GCF_001280255.1:WP_053767937.1   1 MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSPIRHILVRHEQGGIHAATAYARASGRVGVVMATSGP 73 
                                           89*********************************************************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Ga nlvtg+a+a +ds+P+v++tG v+++liG+dafqe+d++G+t+p+tkh++lv++++++p+++keaf+ias
  NCBI__GCF_001280255.1:WP_053767937.1  74 GALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTMPITKHNYLVQDVNEIPRVVKEAFHIAS 146
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPvl+dlPkdv+ ae++ e + +++lpgykpt++gh++qi++al+++eka++P+l+vGgG+ +  a++e
  NCBI__GCF_001280255.1:WP_053767937.1 147 TGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGYKPTLRGHPKQIERALDALEKAERPILMVGGGAQH--AHAE 217
                                           ****************************************************************976..5679 PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           l  +ae++ +pv+ttl+GlGafp +hpl lgm GmhGt +an a+++ad+++a+G rfddrvtg++++fap+a
  NCBI__GCF_001280255.1:WP_053767937.1 218 LLAFAEKTGLPVITTLMGLGAFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHA 290
                                           ************************************************************************9 PP

                             TIGR00118 293 k.iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPq 364
                                           + iih+didPaeigk+v+++ipivGd++ vl+e+lk +k  +     W++++eew+++y+l++  + +  +  
  NCBI__GCF_001280255.1:WP_053767937.1 291 HtIIHVDIDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAKPLRLAA--WWRELEEWRTRYPLRYRPRPHLQA-P 360
                                           769**********************************99999888..*************99988776555.5 PP

                             TIGR00118 365 kvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437
                                           +vi++ ++ + ++aivtt+vGqhqm+aaq++++++pr+f+tsgGlGtmG GlP a+Ga++a pee v++ +Gd
  NCBI__GCF_001280255.1:WP_053767937.1 361 EVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMGVGLPFAIGAQIARPEELVIDFDGD 433
                                           8************************************************************************ PP

                             TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriek 510
                                           gsfqm+lqel+t+v+y +pvk+vilnn +lGmv+qWq+lf+ +ryse++la ++pdf+klaeayG+kg+r+e+
  NCBI__GCF_001280255.1:WP_053767937.1 434 GSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQWQDLFHAKRYSEVYLADSNPDFAKLAEAYGIKGVRVER 506
                                           ************************************************************************* PP

                             TIGR00118 511 peeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           +e+l++ ++ +l+ ++pv+ +++v +ee v+Pm++ G++ ++++ 
  NCBI__GCF_001280255.1:WP_053767937.1 507 KEDLKKGVEAVLNADGPVVAEFKVYHEEGVFPMIPAGGAAEDMIL 551
                                           ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (561 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.99
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis